Feels like a flat but it's not.....
 

Riding over roots and rocks I feel a thump in the rear end. Feels very similar to a flat tire and having the rim bottom out on the root or rock. Wondering if it could be the hub? It's a cannondale fire, and there is a small amount of play side to side in the hub. But I wouldn't think it could magnify its self to the point that I am feeling it thump as bad as I am. Maybe it's the shock but it holds air just fine and seems to compress and rebound fine as well.

Check the rear suspension pivot bolts. Do you have the proper tire pressure?

Mebbe the wheel is loose and the noise is the axle hitting the dropouts. Or could even be the deraileur or something attached...

If the axle is tight in the dropouts and the wheel moves side to side you need to adjust/replace the bearings.

i have brand new white industries hubs with no slop in the bearings and have the same issue. its unnerving. i rode the same tire/rim combo with a different hub (with shot bearings) on a different bike, and the problem was nonexsistant. the rear tire constantly feels flat or like its pinch flatting, but its not, so i just try to ignore it. (both bikes are steel, both rims 717s, both wheels use xl 14 spokes... kenda karma dtc tires...)